Generally, breaking down a large assembly into smaller assemblies is what I recommend and also practice. Because I like to develop parts in context and like Fusion 360's top down design abilities I don't create everything as a separate file, but that is personal preference, not necessarily "best practice".
I only got around to load down your design this morning and have not had the time to go through it in detail.
It is indeed a very "clean" design with no warnings or errors in the timeline, and everything seems to be properly joined.
Can you describe in more detail what problems you encountered in this design ? Are those performance problems, e.g. in creating joints, or moving assemblies etc. ?
Your design has over 2000 components with more than 8000 bodies. I am assuming that most of the multibody components consist of many hundreds of surface bodies. Is that correct ?